Hello,

I have installed the VS Code extension from the marketplace, and it seems to be installed successfully. But there's no color coding for *.rdm files and no option "Transform this file" when right-clicking on *.rdm files (in File Exporter or VS Code).

Any help would be appreciated.

Thank you in advance.

Redmatch does not currently support repeatable instruments. This functionality might be useful in scenarios where multiple elements need to be captured, such as genomic test results, for example.

A transformation can fail when a rule references a value that is not set. The correct behaviour should be to ignore the attribute.

At the moment, users need to use the command line application to run the actual transformation. It would be good if this functionality was supported directly in the IDE.

Similar to FHIR Shorthand, using aliases can help make rules more readable. For example, in FSH you can define aliases like this:

Alias: SCT = http://snomed.info/sct

Then you can use the alias instead of the full URI.

The compiler is generating an invalid error when a reference to a resource type points at a profile. For example, a reference of type Encounter that points at a profile of Encounter should be valid.

There seems to be a problem where the following error gets thrown upon the first run of the plugin:

Exception in thread "main" java.lang.reflect.InvocationTargetException
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:49)
    at org.springframework.boot.loader.Launcher.launch(Launcher.java:108)
    at org.springframework.boot.loader.Launcher.launch(Launcher.java:58)
    at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:88)
Caused by: java.lang.RuntimeException: There was a problem loading FHIR basic types.
    at au.csiro.redmatch.exporter.HapiReflectionHelper.init(HapiReflectionHelper.java:112)
    at au.csiro.redmatch.exporter.HapiReflectionHelper.<init>(HapiReflectionHelper.java:59)
    at au.csiro.redmatch.lsp.RedmatchLanguageServer.<init>(RedmatchLanguageServer.java:48)
    at au.csiro.redmatch.lsp.Application.main(Application.java:26)
    ... 8 more
Caused by: java.nio.file.NoSuchFileException: /Users/obr187/.fhir/packages/hl7.fhir.r4.core#4.0.1/package
    at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:92)
    at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
    at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:116)
    at java.base/sun.nio.fs.UnixFileAttributeViews$Basic.readAttributes(UnixFileAttributeViews.java:55)
    at java.base/sun.nio.fs.UnixFileSystemProvider.readAttributes(UnixFileSystemProvider.java:149)
    at java.base/java.nio.file.Files.readAttributes(Files.java:1764)
    at java.base/java.nio.file.FileTreeWalker.getAttributes(FileTreeWalker.java:219)
    at java.base/java.nio.file.FileTreeWalker.visit(FileTreeWalker.java:276)
    at java.base/java.nio.file.FileTreeWalker.walk(FileTreeWalker.java:322)
    at java.base/java.nio.file.FileTreeIterator.<init>(FileTreeIterator.java:71)
    at java.base/java.nio.file.Files.walk(Files.java:3825)
    at java.base/java.nio.file.Files.walk(Files.java:3879)
    at au.csiro.redmatch.util.FhirUtils.getStructureDefinitions(FhirUtils.java:42)
    at au.csiro.redmatch.exporter.HapiReflectionHelper.init(HapiReflectionHelper.java:68)
    ... 11 more

Given that Redmatch is already using a terminology server, it would be useful if the compiler would check that concept literals are valid.

When I run mvn clean verify I get error from the server as stated below: I've tried to install

[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO]
[INFO] Redmatch
[INFO] Redmatch UI
[INFO] Redmatch Server
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building Redmatch 1.3.4
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ redmatch ---
[INFO]
[INFO] --- maven-resources-plugin:3.1.0:copy-resources (copy-resources) @ redmatch ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 2 resources
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building Redmatch UI 1.3.4
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ ui ---
[INFO]
[INFO] --- exec-maven-plugin:3.0.0:exec (exec-yarn-install) @ ui ---
yarn install v1.22.17
warning ../../../../../package.json: No license field
[1/4] Resolving packages...
success Already up-to-date.
Done in 0.56s.
[INFO]
[INFO] --- exec-maven-plugin:3.0.0:exec (exec-yarn-antlr4ts) @ ui ---
yarn run v1.22.17
warning ../../../../../package.json: No license field
$ antlr4ts -visitor src/grammar/au/csiro/redmatch/grammar/RedmatchLexer.g4 src/grammar/au/csiro/redmatch/grammar/RedmatchGrammar.g4
Generating file '/Users/ethelschinedu/fhirGenomics/fhirGenomeApp/redMatch/redmatch/ui/src/grammar/au/csiro/redmatch/grammar/RedmatchLexer.interp' for grammar 'src/grammar/au/csiro/redmatch/grammar/RedmatchLexer.g4'
Generating file '/Users/ethelschinedu/fhirGenomics/fhirGenomeApp/redMatch/redmatch/ui/src/grammar/au/csiro/redmatch/grammar/RedmatchLexer.ts' for grammar 'src/grammar/au/csiro/redmatch/grammar/RedmatchLexer.g4'
Generating file '/Users/ethelschinedu/fhirGenomics/fhirGenomeApp/redMatch/redmatch/ui/src/grammar/au/csiro/redmatch/grammar/RedmatchLexer.tokens' for grammar 'src/grammar/au/csiro/redmatch/grammar/RedmatchLexer.g4'
Generating file '/Users/ethelschinedu/fhirGenomics/fhirGenomeApp/redMatch/redmatch/ui/src/grammar/au/csiro/redmatch/grammar/RedmatchGrammar.interp' for grammar 'src/grammar/au/csiro/redmatch/grammar/RedmatchGrammar.g4'
Generating file '/Users/ethelschinedu/fhirGenomics/fhirGenomeApp/redMatch/redmatch/ui/src/grammar/au/csiro/redmatch/grammar/RedmatchGrammar.ts' for grammar 'src/grammar/au/csiro/redmatch/grammar/RedmatchGrammar.g4'
Generating file '/Users/ethelschinedu/fhirGenomics/fhirGenomeApp/redMatch/redmatch/ui/src/grammar/au/csiro/redmatch/grammar/RedmatchGrammarListener.ts' for grammar 'src/grammar/au/csiro/redmatch/grammar/RedmatchGrammar.g4'
Generating file '/Users/ethelschinedu/fhirGenomics/fhirGenomeApp/redMatch/redmatch/ui/src/grammar/au/csiro/redmatch/grammar/RedmatchGrammarVisitor.ts' for grammar 'src/grammar/au/csiro/redmatch/grammar/RedmatchGrammar.g4'
Generating file '/Users/ethelschinedu/fhirGenomics/fhirGenomeApp/redMatch/redmatch/ui/src/grammar/au/csiro/redmatch/grammar/RedmatchGrammar.tokens' for grammar 'src/grammar/au/csiro/redmatch/grammar/RedmatchGrammar.g4'
Done in 0.92s.
[INFO]
[INFO] --- exec-maven-plugin:3.0.0:exec (exec-yarn-build) @ ui ---
yarn run v1.22.17
warning ../../../../../package.json: No license field
$ react-app-rewired build
Creating an optimized production build...
Browserslist: caniuse-lite is outdated. Please run the following command: npx browserslist --update-db
Compiled with warnings.

src/api/RedmatchApi.ts
Line 9:10: 'AxiosResponse' is defined but never used @typescript-eslint/no-unused-vars
Line 10:10: 'IParameters' is defined but never used @typescript-eslint/no-unused-vars
Line 68:1: Assign arrow function to a variable before exporting as module default import/no-anonymous-default-export

src/components/CodeSearch.tsx
Line 72:13: 'ServerResponse' is defined but never used @typescript-eslint/no-unused-vars

Search for the keywords to learn more about each warning.
To ignore, add // eslint-disable-next-line to the line before.

File sizes after gzip:

862.75 KB build/static/js/2.a16a9a91.chunk.js
73.6 KB build/json.worker.js
44.03 KB build/editor.worker.js
28.84 KB build/static/js/3.0f82bb1b.chunk.js
20.42 KB build/static/js/main.a8940e43.chunk.js
12.5 KB build/static/css/2.92855bb5.chunk.css
1.17 KB build/static/js/runtime-main.2126936a.js
278 B build/static/css/main.6dea0f05.chunk.css

The project was built assuming it is hosted at /.
You can control this with the homepage field in your package.json.

The build folder is ready to be deployed.
You may serve it with a static server:

yarn global add serve
serve -s build

Find out more about deployment here:

https://cra.link/deployment

Done in 45.92s.
[INFO]
[INFO] --- maven-resources-plugin:3.1.0:copy-resources (copy-resources) @ ui ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /Users/ethelschinedu/fhirGenomics/fhirGenomeApp/redMatch/redmatch/ui/server/src/main/antlr4
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building Redmatch Server 1.3.4
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ server ---
[INFO] Deleting /Users/ethelschinedu/fhirGenomics/fhirGenomeApp/redMatch/redmatch/server/target
[INFO]
[INFO] --- build-helper-maven-plugin:3.2.0:add-source (default) @ server ---
[INFO] Source directory: /Users/ethelschinedu/fhirGenomics/fhirGenomeApp/redMatch/redmatch/server/target/generated-sources/antlr4/java added.
[INFO]
[INFO] --- maven-resources-plugin:3.1.0:copy-resources (copy-resources) @ server ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /Users/ethelschinedu/fhirGenomics/fhirGenomeApp/redMatch/redmatch/server/server/src/main/antlr4
[INFO]
[INFO] --- antlr4-maven-plugin:4.8-1:antlr4 (antlr-java) @ server ---
[INFO] ANTLR 4: Processing source directory /Users/ethelschinedu/fhirGenomics/fhirGenomeApp/redMatch/redmatch/server/src/main/antlr4
[INFO] Processing grammar: au/csiro/redmatch/grammar/RedmatchLexer.g4
[INFO] Processing grammar: au/csiro/redmatch/grammar/RedmatchGrammar.g4
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] Redmatch ........................................... SUCCESS [ 0.278 s]
[INFO] Redmatch UI ........................................ SUCCESS [ 48.213 s]
[INFO] Redmatch Server .................................... FAILURE [ 1.338 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 50.211 s
[INFO] Finished at: 2021-11-17T16:58:27+00:00
[INFO] Final Memory: 33M/381M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:license-maven-plugin:2.0.0:add-third-party (add-third-party) on project server: The plugin org.codehaus.mojo:license-maven-plugin:2.0.0 requires Maven version 3.5.4 -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/PluginIncompatibleException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR] mvn -rf :server

I noticed some issues with yarn add -W caniuse-lite and have tried to resolve it and getting

error An unexpected error occurred: "https://registry.yarnpkg.com/hl7.fhir.us.mcode: Not found".

Please, is there any help you can offer?

It would be useful to implement quick fixes for the VS Code plugin to enhance the user experience. This could include adding mising mappings, suggesting valid ids, etc.

Hello,

i've had a few problems following the installation tutorial.
First problem: Dead Link for redcap dictionary (FIXED: can be found manually)
Secound problem: Dictonary has doubles in it (FIXED: you have to rename a few variables yourself before uploading)
Third (UNFIXED) problem: Error during

maven clean verify :

(---------- SNIPPLET -------------)
[INFO] Building Redmatch UI 1.3.4 [2/3]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO]
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ ui ---
[INFO]
[INFO] --- exec-maven-plugin:3.0.0:exec (exec-yarn-install) @ ui ---
yarn install v1.22.10
warning ../package.json: No license field
[1/4] Resolving packages...
success Already up-to-date.
Done in 0.99s.
[INFO]
[INFO] --- exec-maven-plugin:3.0.0:exec (exec-yarn-antlr4ts) @ ui ---
yarn run v1.22.10
warning ../package.json: No license field
$ antlr4ts -visitor src/grammar/au/csiro/redmatch/grammar/RedmatchLexer.g4 src/grammar/au/csiro/redmatch/grammar/RedmatchGrammar.g4
error(7): cannot find or open file: src/grammar/au/csiro/redmatch/grammar/RedmatchLexer.g4
error(7): cannot find or open file: src/grammar/au/csiro/redmatch/grammar/RedmatchGrammar.g4
child process exited with code 1
error Command failed with exit code 1.
info Visit https://yarnpkg.com/en/docs/cli/run for documentation about this command.
[ERROR] Command execution failed.
(---------- END OF SNIPPLET -------------)

It feels like some files in the repo have been moved incorrectly? Can someone help me with this issue?
Thanks in advance

Cheers Raphael

The Redmatch backend is capable of importing and exporting the mappings in Excel format, but this functionality is not exposed in the frontend. This would enable the use of external tools that provide automated mapping functionality.

The VALUE function has no way of removing potentially identifying information in dates. This is useful if the information in the target FHIR repository needs to be de-identified.

Redmatch currently uses the same metadata model used by REDCap. The application should be refactored to use a generic metadata model so it is easier to support other data sources in the future.

It would be good if the calculation of the mappings took into account conditions like VALUE(xx) != 3 and a CONCEPT_SELECTED used in the body of the rules. This pattern is quite common if the author is only intersted in some of the values of a drop down box, for example, if only abnormal values trigger the creation of FHIR resources. At the moment the mappings include all the values of the drop down box, even though in this case value 3 will never be assigned.

REDCap dropbox fields can be configured to support autocomplete and the type then becomes AUTOCOMPLETE. This is currently ignored by Redmatch and a type of NONE is assigned. SQL queries are also currently unsupported in Redmatch and these can also be turned into AUTOCOMPLETE fields.

The error messages at the REST API level could be more detailed. At the moment only a string is returned. It would be better to return structured JSON, like in FHIR or like the GitHub API, e.g.,

HTTP/1.1 422 Unprocessable Entity
Content-Length: 149

{
  "message": "Validation Failed",
  "errors": [
    {
      "resource": "Issue",
      "field": "title",
      "code": "missing_field"
    }
  ]
}

The application should support IGs in the following way:

• A code system for validation should be created based on the IG
  • The IG should be based on the current supported FHIR version
  • The main grammar should work fine, but the validation needs to be updated
• The validation and autocomplete functionality (when implemented) should support referring to any extensions through shortcuts based on the names defined in the IG
• The FHIR exporter needs to identify that a path shortcut is an extension to create the extensions in FHIR
• The validator should be aware of profiles and issue errors accordingly

When a mapping is missing and it is added using a quick fix, the label is not being escaped.

For example:

cmdt_result___1|'A cause for this patient's condition has not been identified' -> http://snomed.info/sct|138875005|'SNOMED CT Concept'; should be cmdt_result___1|'A cause for this patient\'s condition has not been identified' -> http://snomed.info/sct|138875005|'SNOMED CT Concept';

Also, a warning is being shown when the user manually escapes the string.

Hello,

i tried to install redmatch onto a virtual machine, so that multiple parties can access and try it out. In the end it even showed a loading screen which then redirected to localhost (on client PC) which obviously had no service (i think it was for keycloak) running.
Is there a server configuration/version available? This would be very helpful, probably also for other people who can not install it on a local machine. Or is there an easy fix to suppress the redirection to local machine? Maybe just put in an option for an IP instead of the localhost reference?
Thanks in advance!

Cheers Raphael

It would be useful for users writing rules to have autocomplete support in the rules editor.

A PUT operation with a project resource that has all required fields should create the project if it doesn't exist. Also, a POST operation with a project should be rejected if it contains an id and if a complete project is POSTed then the system should not create the project in the usual way but rather copy all its contents.

Redmatch creates a single resource when a rule does not reference any REDCap fields. However, the behaviour when a rule has a reference to another resource is incorrect. Currently Redmatch creates a single resource if no other attributes reference any fields, regardless of whether the referenced resource is a single resource or not. When the referenced resource is created by a set of rules that do reference REDCap fields and hence multiple resources instances are created, multiple referencing resources should also be created.

The log file is stored in a fixed path, instead of being saved in the USER_HOME/.redmatch folder.

At the moment there is no way of visualising the result of the transformation, i.e., the FHIR resources, until they are uploaded to a FHIR server. It would be useful to be able to generate a visualisation in Redmatch so the author can verify that the rules are in fact producing the desired outcome.

The compiler could look at the definitions of FHIR resources and warn the user if a reference has been specified to a resource that doesn't exist. For example,

TRUE { Patient<p>: * identifier.type.text = 'Medicare Number' }
TRUE { Observation<sex>: * subject = REF(Patient<r>) }

should generate an error highlighting that no resource Patient<r> exists.

The right click command in the VSCode plugin doesn't seem to be working properly and only the output of the last file that is processed seems to be saved.

After refactoring the way the application is packaged, setting environment variables for the UI component in Docker no longer works properly.

Currently, only the data from a single project can be exported at a time. This means that data has to be merged externally. It would be good to have the option of exporting data from multiple projects as a single collection of ND-JSON files.

Currently, mappings are not being validated. This is not problematic if the mappings are generated using the UI because the UI uses the terminology server to find the target concepts, so these will be valid. However, if the mappings are loaded using an Excel spreadsheet, then some of these might be invalid and the target FHIR representation might include invalid concepts.

There seem to be some circumstances where existing mappings disappear unexpectedly. I suspect this has to do with a case where the rules are saved with errors and therefore the system assumes no mappings are necessary and thus erases any current mappings. This is obviously the expected behaviour.

Hello! I am a graduate student researcher with Columbia University's Department of Biomedical Informatics and I am looking to integrate Redmatch as part of a larger clinical data interoperability pipeline. I have been deploying this through Docker on my local machine along with a HAPI FHIR server. However, I have been running into some issues when trying to create a new project in Redmatch.

Initially, I was running into this error that would pop-up immediately after logging in as well as when clicking 'Save': Unable to create new project: TypeError: Cannot read property 'status' of undefined

Due to the limitations of the implementation of the HAPI server I am working with, I had to try and switch Redmatch off 8080 to a different port, but I couldn't avoid getting this error. It also seemed to be consistently associated with a call to localhost:8082/project and I didn't see anywhere in the code a direct call to this port. The one spot I could find was in the React code referring to the environmental variable as defined in the Dockerfile, which did not mention 8082. I could not get it to work even being the only Docker container running.

I stepped away from this for a week or so, but then today when I went to run Redmatch alone again, I did not see the undefined error. However, today I did not have that error and instead ran into this 502 error: Unable to create new project: Error: Request failed with status code 502

Would you be able to help me diagnose either of these issues (if the first were to come up again)? Thank you!